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Segmentation fault when running test_common.py::test_estimators[NuSVC()-check_classifiers_train(readonly_memmap=True)]

See original GitHub issue

Describe the bug

I followed the contributing code guidelines and ran into a segmentation fault when running the test sklearn/tests/test_common.py. It appears to come from libsvm.fit(...).

I am not sure whether it is a problem related to my device or not.

Steps/Code to Reproduce

git clone https://github.com/scikit-learn/scikit-learn.git
cd scikit-learn
python3 -m venv venv
source venv/bin/activate
pip install pip --upgrade
pip install numpy scipy matplotlib pytest sphinx cython ipykernel
pip install --no-build-isolation --editable .
pytest sklearn/tests/test_common.py

Expected Results

No error is thrown.

Actual Results

Fatal Python error: Segmentation fault

Current thread 0x00007fe406b46280 (most recent call first):
  File "/home/aperez/dev/sandbox/scikit-learn/sklearn/svm/_base.py", line 315 in _dense_fit
  File "/home/aperez/dev/sandbox/scikit-learn/sklearn/svm/_base.py", line 255 in fit
  File "/home/aperez/dev/sandbox/scikit-learn/sklearn/utils/estimator_checks.py", line 2091 in check_classifiers_train
  File "/home/aperez/dev/sandbox/scikit-learn/sklearn/utils/_testing.py", line 313 in wrapper
  File "/home/aperez/dev/sandbox/scikit-learn/sklearn/tests/test_common.py", line 109 in test_estimators
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/python.py", line 183 in pytest_pyfunc_call
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/python.py", line 1641 in runtest
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 162 in pytest_runtest_call
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 255 in <lambda>
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 311 in from_call
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 254 in call_runtest_hook
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 215 in call_and_report
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 126 in runtestprotocol
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/runner.py", line 109 in pytest_runtest_protocol
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/main.py", line 348 in pytest_runtestloop
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/main.py", line 323 in _main
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/main.py", line 269 in wrap_session
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/config/__init__.py", line 162 in main
  File "/home/aperez/dev/sandbox/scikit-learn/venv/lib/python3.8/site-packages/_pytest/config/__init__.py", line 185 in console_main
  File "/home/aperez/dev/sandbox/scikit-learn/venv/bin/pytest", line 8 in <module>
Erreur de segmentation (core dumped)

Versions

System:
    python: 3.8.10 (default, May 27 2021, 17:54:13)  [GCC 9.3.0]
executable: /home/aperez/dev/sandbox/scikit-learn/venv/bin/python
   machine: Linux-5.13.0-1014-oem-x86_64-with-glibc2.29

Python dependencies:
          pip: 21.3
   setuptools: 56.0.0
      sklearn: 1.1.dev0
        numpy: 1.21.2
        scipy: 1.7.1
       Cython: 0.29.24
       pandas: None
   matplotlib: 3.4.3
       joblib: 1.1.0
threadpoolctl: 3.0.0

Built with OpenMP: True